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Artigos de revistas sobre o tema "RNA signature"

Autor: Grafiati

Publicado: 12 de abril de 2025

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1

Liu, Jie, Wenmin Deng, Zhiwen Xiao, Xiaofeng Huang, Minmin Lin, and Zhen Long. "Identification of RNA Modification-Associated Alternative Splicing Signature as an Independent Factor in Head and Neck Squamous Cell Carcinoma." Journal of Immunology Research 2022 (September 13, 2022): 1–19. http://dx.doi.org/10.1155/2022/8976179.

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Objective. Head and neck squamous cell carcinoma (HNSCC) is a highly heterotopic malignant tumor. Alternative splicing (AS) and RNA modification have been reported to be involved in tumorigenesis. Therefore, we constructed RNA modification-associated AS (RMA-AS) signature model to predict the prognosis of HNSCC. Methods. AS events and RNA-modified gene expression information were downloaded from TCGA-HNSCC database. Univariate Cox regression analysis was employed for analyzing prognosis-related AS events. RMA-AS events were obtained by constructing a coexpression network between RNA modificati

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Stupnikov, Alexey, Paul G. O’Reilly, Caitriona E. McInerney, et al. "Impact of Variable RNA-Sequencing Depth on Gene Expression Signatures and Target Compound Robustness: Case Study Examining Brain Tumor (Glioma) Disease Progression." JCO Precision Oncology, no. 2 (November 2018): 1–17. http://dx.doi.org/10.1200/po.18.00014.

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Purpose Gene expression profiling can uncover biologic mechanisms underlying disease and is important in drug development. RNA sequencing (RNA-seq) is routinely used to assess gene expression, but costs remain high. Sample multiplexing reduces RNA-seq costs; however, multiplexed samples have lower cDNA sequencing depth, which can hinder accurate differential gene expression detection. The impact of sequencing depth alteration on RNA-seq–based downstream analyses such as gene expression connectivity mapping is not known, where this method is used to identify potential therapeutic compounds for

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Albitar, Maher, Sally Agersborg, Ahmad Charifa, et al. "Establishing Distinct Cytokine Signatures Differentiating between Acute Myeloid Leukemia, Myelodysplastic Syndrome, and Chip Using Bone Marrow RNA or Cell-Free RNA (cfRNA)." Blood 144, Supplement 1 (2024): 4295. https://doi.org/10.1182/blood-2024-203870.

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Cytokines are essential for various immune functions and the overall inflammatory response to myeloid neoplasms in bone marrow. They play a major role in bone marrow microenvironment in normal and abnormal hematopoiesis. Cytokines exert their functions by interacting with their receptors, and full evaluation of the cytokines' roles requires evaluating their receptors as well. Using next generation sequencing (NGS) and machine learning, we measured the expression of 36 cytokines/chemokines and cytokine receptors in the bone marrow (BM) of patients with acute myeloid leukemia (AML), myelodysplas

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Al Mahi, Naim, Erik Y. Zhang, Susan Sherman, Jane J. Yu, and Mario Medvedovic. "Connectivity Map Analysis of a Single-Cell RNA-Sequencing -Derived Transcriptional Signature of mTOR Signaling." International Journal of Molecular Sciences 22, no. 9 (2021): 4371. http://dx.doi.org/10.3390/ijms22094371.

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In the connectivity map (CMap) approach to drug repositioning and development, transcriptional signature of disease is constructed by differential gene expression analysis between the diseased tissue or cells and the control. The negative correlation between the transcriptional disease signature and the transcriptional signature of the drug, or a bioactive compound, is assumed to indicate its ability to “reverse” the disease process. A major limitation of traditional CMaP analysis is the use of signatures derived from bulk disease tissues. Since the key driver pathways are most likely dysregul

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Lu, Zhihao, Huan Chen, Shuang Li, et al. "A RNA signature predicts outcomes in immune checkpoint blockade treated gastrointestinal cancer patients." Journal of Clinical Oncology 37, no. 15_suppl (2019): e14071-e14071. http://dx.doi.org/10.1200/jco.2019.37.15_suppl.e14071.

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e14071 Background: Cancer therapy has been greatly revolutionized in recent years by the conceptual developments in the field of cancer immunology. Growing evidence support the utility of immune checkpoint inhibition (ICB) in gastrointestinal (GI) cancer. However, a central question lies in understanding how therapeutic responsiveness is predicted. Methods: To address this, we evaluated tumor FFPE specimens from 97 patients who received ICB treatment. All patients were randomly assigned into discovery (60%) and validation (40%) cohorts. Tumor RNA before ICB treatment was analyzed on a multiple

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Li, Chenyang, Thinh T. Nguyen, Jian-Rong Li, et al. "Abstract 97: Multiregional profiling revealed intra-tumor transcriptomic heterogeneity associated with the prognosis in non-small cell lung cancer." Cancer Research 83, no. 7_Supplement (2023): 97. http://dx.doi.org/10.1158/1538-7445.am2023-97.

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Abstract Introduction: Intratumor heterogeneity (ITH) describes the distinct tumor cell populations and microenvironments within the same tumor, which may profoundly impact cancer evolution and clinical outcomes. Non-small cell lung cancer (NSCLC) is not only a genetically diverse disease but also has high transcriptomic heterogeneity (RNA-ITH). The RNA-ITH limits the reproducibility of expression-based prognostic models, which is poorly understood. Methods: To address the issue, we investigated the effect of RNA-ITH on prognosis at both gene and signature levels using multiregional RNA-seq da

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Wen, Huaming, Ryan A. Gallo, Xiaosheng Huang, et al. "Incorporating Differential Gene Expression Analysis with Predictive Biomarkers to Identify Novel Therapeutic Drugs for Fuchs Endothelial Corneal Dystrophy." Journal of Ophthalmology 2021 (June 28, 2021): 1–8. http://dx.doi.org/10.1155/2021/5580595.

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Purpose. Based on the differential gene expression analysis for predictive biomarkers with RNA-Sequencing data from Fuchs endothelial corneal dystrophy (FECD) patients, we are aiming to evaluate the efficacy of Library of Integrated Network-based Cellular Signatures (LINCS) perturbagen prediction software to identify novel pharmacotherapeutic targets that can revert the pathogenic gene expression signatures and reverse disease phenotype in FECD. Methods. A publicly available RNA-seq dataset was used to compare corneal endothelial specimens from controls and patients with FECD. Based on the dif

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Wang, Kang, Yajing Zhu, Ioannis Zerdes, et al. "Abstract PO2-07-06: Multimodal learning predictor of HER2-positive breast cancer therapy response in the randomized PREDIX HER2 trial." Cancer Research 84, no. 9_Supplement (2024): PO2–07–06—PO2–07–06. http://dx.doi.org/10.1158/1538-7445.sabcs23-po2-07-06.

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Abstract Background: The PREDIX HER2 trial, compared six courses of docetaxel, trastuzumab, and pertuzumab (DTP) vs. trastuzumab emtansine (T-DM1) as neoadjuvant treatment for HER2-positive breast cancer (BC). Similar rates of pathologic complete response (pCR) were seen. Methods: Clinicopathological, shallow whole-genome sequencing (CUTseq, n=176), whole exome sequencing (WES, n=192), and RNA-sequencing (RNA-seq, n=187) data were generated using fresh-frozen baseline core biopsies. Potential tumor intrinsic resistance factors and microenvironment components were quantified by multi-omics anal

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Erbe, Rossin, Michelle M. Stein, Tim A. Rand, and Justin Guinney. "Abstract 2281: A tumor-intrinsic signature involving immunosuppression via MIF-CD74 signaling is associated with overall survival in ICT-treated lung adenocarcinoma." Cancer Research 84, no. 6_Supplement (2024): 2281. http://dx.doi.org/10.1158/1538-7445.am2024-2281.

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Abstract Introduction: Immune checkpoint therapies (ICT) have changed cancer care, yielding robust and durable responses in a subset of patients. Identifying patients who are likely to respond to ICT remains an ongoing challenge. In addition, only a portion of patients with clinical biomarkers respond to therapy. Signatures of RNA expression have been developed to predict response, the majority of which focus on T-cell and cytotoxicity markers, yet have been unable to substantially improve outcome predictions. Here, we present a RNA signature that instead describes tumor-intrinsic immune resis

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Qiu, Lipeng, Tao Wang, Qi Ge, et al. "Circular RNA Signature in Hepatocellular Carcinoma." Journal of Cancer 10, no. 15 (2019): 3361–72. http://dx.doi.org/10.7150/jca.31243.

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Pačínková, Anna, and Vlad Popovici. "Cross-platform Data Analysis Reveals a Generic Gene Expression Signature for Microsatellite Instability in Colorectal Cancer." BioMed Research International 2019 (March 17, 2019): 1–9. http://dx.doi.org/10.1155/2019/6763596.

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The dysfunction of the DNA mismatch repair system results in microsatellite instability (MSI). MSI plays a central role in the development of multiple human cancers. In colon cancer, despite being associated with resistance to 5-fluorouracil treatment, MSI is a favourable prognostic marker. In gastric and endometrial cancers, its prognostic value is not so well established. Nevertheless, recognising the MSI tumours may be important for predicting the therapeutic effect of immune checkpoint inhibitors. Several gene expression signatures were trained on microarray data sets to understand the reg

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Allen, Hermione E., Andrew McIntyre, Jesus Gutierrez-Abril, et al. "The Role of the Bone Marrow Immune Niche in Preventing Relapse in Adult B-ALL Following Reduced Intensity Conditioning Allogeneic HSCT." Blood 144, Supplement 1 (2024): 1454. https://doi.org/10.1182/blood-2024-205516.

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Reduced intensity-conditioned allogeneic haematopoietic stem cell transplants (alloHSCT) improved event-free survival for patients with B-cell acute lymphoblastic leukaemia (B-ALL) &gt;40 years old, as established by the UKALL14 trial (Marks et al. 2022) The main factor predicting outcome post alloHSCT was persistence of minimal residual disease (MRD). Other studies also find that MRD to be a strong predictor of relapse after alloHSCT in ALL (Della Starza et al., 2019) which is associated with an ineffective graft-versus-leukaemia (GVL) response by donor T cells (Rosko et al., 2016); (Lin

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Narjala, Anushree, Ashwin Nair, Varsha Tirumalai, G. Vivek Hari Sundar, and Padubidri V. Shivaprasad. "A conserved sequence signature is essential for robust plant miRNA biogenesis." Nucleic Acids Research 48, no. 6 (2020): 3103–18. http://dx.doi.org/10.1093/nar/gkaa077.

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Abstract Micro (mi)RNAs are 20–22nt long non-coding RNA molecules involved in post-transcriptional silencing of targets having high base-pair complementarity. Plant miRNAs are processed from long Pol II-transcripts with specific stem-loop structures by Dicer-like (DCL) 1 protein. Although there were reports indicating how a specific region is selected for miRNA biogenesis, molecular details were unclear. Here, we show that the presence of specific GC-rich sequence signature within miRNA/miRNA* region is required for the precise miRNA biogenesis. The involvement of GC-rich signatures in precise

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Farias Amorim, Camila, Fernanda O. Novais, Ba T. Nguyen та ін. "Localized skin inflammation during cutaneous leishmaniasis drives a chronic, systemic IFN-γ signature". PLOS Neglected Tropical Diseases 15, № 4 (2021): e0009321. http://dx.doi.org/10.1371/journal.pntd.0009321.

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Cutaneous leishmaniasis is a localized infection controlled by CD4+ T cells that produce IFN-γ within lesions. Phagocytic cells recruited to lesions, such as monocytes, are then exposed to IFN-γ which triggers their ability to kill the intracellular parasites. Consistent with this, transcriptional analysis of patient lesions identified an interferon stimulated gene (ISG) signature. To determine whether localized L. braziliensis infection triggers a systemic immune response that may influence the disease, we performed RNA sequencing (RNA-seq) on the blood of L. braziliensis-infected patients an

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McDermott, David F., Jae-Lyun Lee, Georg A. Bjarnason, et al. "Evaluation of RNA-sequencing (RNA-seq) signatures with pembrolizumab (pembro) in patients (pts) with renal cell carcinoma (RCC) from KEYNOTE-427 cohort A." Journal of Clinical Oncology 38, no. 6_suppl (2020): 729. http://dx.doi.org/10.1200/jco.2020.38.6_suppl.729.

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729 Background: We evaluated the association (assoc) of baseline RNA-seq–based signatures with response/resistance to pembro from the phase 2 KEYNOTE-427 study (NCT02853344) in pts with advanced clear cell RCC enrolled in cohort A (n = 110). Methods: In pembro-treated pts with RNA-seq and clinical data (N = 78), we analyzed the assoc of signatures (18-gene tumor T-cell–inflamed GEP; 10 non–T-cell–inflamed GEP canonical signatures [angiogenesis, gMDSC, glycolysis, hypoxia, mMDSC, MYC, proliferation, RAS, stromal/EMT/TGFβ, WNT]) quantifying the TME with clinical outcomes. Canonical signatures we

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Dolgosheina, E. V., R. D. Morin, G. Aksay, et al. "Conifers have a unique small RNA silencing signature." RNA 14, no. 8 (2008): 1508–15. http://dx.doi.org/10.1261/rna.1052008.

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Chai, Rui-Chao, tao jiang, and Yong-Zhi Wang. "GENE-49. RNA PROCESSING GENES CHARACTERIZE RNA SPLICING AND FURTHER STRATIFY LOWER-GRADE GLIOMA." Neuro-Oncology 21, Supplement_6 (2019): vi108. http://dx.doi.org/10.1093/neuonc/noz175.451.

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Abstract Aberrant expression of RNA processing genes may drive the alterative RNA profile in lower-grade gliomas (LGGs). Thus, we aimed to further stratify LGGs based on the expression of RNA processing genes. This study included 446 LGGs from The Cancer Genome Atlas (TCGA, training set) and 171 LGGs from the Chinese Glioma Genome Atlas (CGGA, validation set). The least absolute shrinkage and selection operator (LASSO) Cox regression algorithm was conducted to develop a risk-signature. The ROC curves and Kaplan–Meier curves were used to study the prognosis value of the risk-signature. Among th

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BYKHOVSKI, ALEXEI, TATIANA GLOBUS, TATYANA KHROMOVA, BORIS GELMONT, and DWIGHT WOOLARD. "AN ANALYSIS OF THE THZ FREQUENCY SIGNATURES IN THE CELLULAR COMPONENTS OF BIOLOGICAL AGENTS." International Journal of High Speed Electronics and Systems 17, no. 02 (2007): 225–37. http://dx.doi.org/10.1142/s012915640700445x.

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The development of an effective biological (bio) agent detection capability based upon terahertz (THz) frequency absorption spectra will require insight into how the constituent cellular components contribute to the overall THz signature. In this work, the specific contribution of ribonucleic acid (RNA) to THz spectra is analyzed in detail. Previously, it has only been possible to simulate partial fragments of the RNA (or DNA) structures due to the excessive computational demands. For the first time, the molecular structure of the entire transfer RNA (tRNA) molecule of E. coli was simulated an

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Davanian, Haleh, Anangi Balasiddaiah, Robert Heymann, et al. "Ameloblastoma RNA profiling uncovers a distinct non-coding RNA signature." Oncotarget 8, no. 3 (2016): 4530–42. http://dx.doi.org/10.18632/oncotarget.13889.

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Zhou, Yao, Xingju Zheng, Zhucheng Sun, and Bo Wang. "Analysis of Bladder Cancer Staging Prediction Using Deep Residual Neural Network, Radiomics, and RNA-Seq from High-Definition CT Images." Genetics Research 2024 (April 30, 2024): 1–11. http://dx.doi.org/10.1155/2024/4285171.

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Bladder cancer has recently seen an alarming increase in global diagnoses, ascending as a predominant cause of cancer-related mortalities. Given this pressing scenario, there is a burgeoning need to identify effective biomarkers for both the diagnosis and therapeutic guidance of bladder cancer. This study focuses on evaluating the potential of high-definition computed tomography (CT) imagery coupled with RNA-sequencing analysis to accurately predict bladder tumor stages, utilizing deep residual networks. Data for this study, including CT images and RNA-Seq datasets for 82 high-grade bladder ca

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Li, Xinyu, Shuqiao Zhang, Shijun Zhang, Weihong Kuang, and Chunzhi Tang. "Inflammatory Response-Related Long Non-Coding RNA Signature Predicts the Prognosis of Hepatocellular Carcinoma." Journal of Oncology 2022 (March 17, 2022): 1–13. http://dx.doi.org/10.1155/2022/9917244.

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Background. Hepatocellular carcinoma (HCC) is a high mortality malignant tumor with genetic and phenotypic heterogeneity, making predicting prognosis challenging. Meanwhile, the inflammatory response is an indispensable player in the tumorigenesis process and regulates the tumor microenvironment, which can affect the prognosis of tumor patients. Methods. Using HCC samples in the TCGA-LIHC dataset, we explored lncRNA expression profiles associated with the inflammatory response. The inflammatory response-related lncRNA signature was constructed by univariate Cox regression, LASSO regression, an

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Baranov, Oleg, Polina Turova, Vladimir Kushnarev, et al. "Closing classification gaps in luminal breast cancer with single-cell RNA-seq insights from normal breast lineages." Journal of Clinical Oncology 42, no. 16_suppl (2024): e13168-e13168. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.e13168.

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e13168 Background: Almost two decades ago, invasive breast cancer was classified into five subgroups based on expression patterns, each with distinct biological and prognostic characteristics. Advances in single-cell RNA sequencing offers insights into the expression profiles of normal luminal epithelial cells. Here, we investigate the connection between breast cancer (BC) classification and luminal expression profiles. Methods: We applied single-cell data from recent studies (Table) to compile gene signatures corresponding to expression profiles of luminal epithelial cell clusters in normal b

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Li, Xuanyi, Ben Ho Park, Justin M. Balko та Douglas Buckner Johnson. "Pathway enrichment analysis in tumors with high mutation burdens and interferon-γ signature expression: A pancancer analysis." Journal of Clinical Oncology 41, № 16_suppl (2023): 3138. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3138.

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3138 Background: Tumor mutation burden (TMB) correlates with immunotherapy response, but outcomes still vary in high TMB cancers, and many high TMB tumors lack T cell infiltration. Here, we assessed gene expression signatures of high TMB, including both inflamed and non-inflamed tumors (defined by interferon-γ [IFN-γ] gene signatures). Methods: Gene set enrichment analysis (GSEA) was assessed from RNA-sequencing data in tumors in TCGA. TMB and IFN-γ signature score were assessed by previously published methods. We performed GSEA on high vs low TMB tumors, and further stratified by high vs low

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Kenarangi, Taiebe, Enayatolah Bakhshi, Kolsoum Inanloo Rahatloo, and Akbar Biglarian. "Identifying Gene Signature in RNA Sequencing Multiple Sclerosis Data." Iranian Rehabilitation Journal 20, no. 2 (2022): 217–24. http://dx.doi.org/10.32598/irj.20.2.1606.1.

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Objectives: Multiple Sclerosis (MS) is a complex central nervous system disease; it is the result of a combination of genetic predispositions and a nongenetic trigger. This study aims to find the gene signatures using a Pareto optimization algorithm for MS RNA sequencing (RNA-seq) data. Methods: This case-control study involved 50 samples (25 MS patients and 25 age-matched healthy individuals) and their GSE profiles (GSE123496) were selected from the National Center for Biotechnology Information Gene Expression Omnibus database. We used Pareto-optimal cluster size identification to find the ge

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Li, Yang, Rongrong Sun, Rui Li, Yonggang Chen, and He Du. "Prognostic Nomogram Based on Circular RNA-Associated Competing Endogenous RNA Network for Patients with Lung Adenocarcinoma." Oxidative Medicine and Cellular Longevity 2021 (August 28, 2021): 1–13. http://dx.doi.org/10.1155/2021/9978206.

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Evidence is increasingly indicating that circular RNAs (circRNAs) are closely involved in tumorigenesis and cancer progression. However, the function and application of circRNAs in lung adenocarcinoma (LUAD) are still unknown. In this study, we constructed a circRNA-associated competitive endogenous RNA (ceRNA) network to investigate the regulatory mechanism of LUAD procession and further constructed a prognostic signature to predict overall survival for LUAD patients. Differentially expressed circRNAs (DEcircRNAs), differentially expressed miRNAs (DEmiRNAs), and differentially expressed mRNAs

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Singhal, Sandeep K., Sarmad Al-Marsoummi, Emilie E. Vomhof-DeKrey, Bo Lauckner, Trysten Beyer, and Marc D. Basson. "Schlafen 12 Slows TNBC Tumor Growth, Induces Luminal Markers, and Predicts Favorable Survival." Cancers 15, no. 2 (2023): 402. http://dx.doi.org/10.3390/cancers15020402.

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The Schlafen 12 (SLFN12) protein regulates triple-negative breast cancer (TNBC) growth, differentiation, and proliferation. SLFN12 mRNA expression strongly correlates with TNBC patient survival. We sought to explore SLFN12 overexpression effects on in vivo human TNBC tumor xenograft growth and performed RNA-seq on xenografts to investigate related SLFN12 pathways. Stable SLFN12 overexpression reduced tumorigenesis, increased tumor latency, and reduced tumor volume. RNA-seq showed that SLFN12 overexpressing xenografts had higher luminal markers levels, suggesting that TNBC cells switched from a

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Dungu, Kia Hee Schultz, Emma Louise Malchau Carlsen, Jonathan Peter Glenthøj, et al. "Host RNA Expression Signatures in Young Infants with Urinary Tract Infection: A Prospective Study." International Journal of Molecular Sciences 25, no. 9 (2024): 4857. http://dx.doi.org/10.3390/ijms25094857.

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Early diagnosis of infections in young infants remains a clinical challenge. Young infants are particularly vulnerable to infection, and it is often difficult to clinically distinguish between bacterial and viral infections. Urinary tract infection (UTI) is the most common bacterial infection in young infants, and the incidence of associated bacteremia has decreased in the recent decades. Host RNA expression signatures have shown great promise for distinguishing bacterial from viral infections in young infants. This prospective study included 121 young infants admitted to four pediatric emerge

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Wang, Jiamin, Han Lin, Mingda Zhou, et al. "The m6A methylation regulator-based signature for predicting the prognosis of prostate cancer." Future Oncology 16, no. 30 (2020): 2421–32. http://dx.doi.org/10.2217/fon-2020-0330.

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Aim: To construct a survival prediction signature for prostate cancer (PC) based on the RNA N6-methyladenosine (m6A) methylation regulator. Materials & methods: This paper explores the interaction network of differentially expressed m6A RNA methylation regulators in PC by Pearson correlation analysis. Univariate Cox risk regression and LASSO regression analysis were used to construct a predictive signature of PC. Kaplan–Meier survival analysis compared the overall survival of the high- and low-risk groups. Results & Conclusion: We first constructed a prognostic two gene signature for P

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Parikesit, Arli Aditya, Imron Imron, Rizky Nurdiansyah, and David Agustriawan. "The Structural Annotations of The Mir-122 Non-Coding RNA from The Tilapia Fish (Oreochromis niloticus)." HAYATI Journal of Biosciences 29, no. 2 (2022): 171–81. http://dx.doi.org/10.4308/hjb.29.2.171-181.

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Tilapia (Oreochromis niloticus) is an important fisheries commodity. Scientific efforts have been done to increase its quality. One of them is staging a premium diet such as a fat-enriched diet. The transcriptomics approach is able to provide the signatures of the diet outcomes by observing the micro(mi)RNA signature in transcriptional regulation. Hence, it was found that the availability of mir-122 is essential in the regulation of a high-fat diet in tilapia. However, this transcriptomics signature is lacking structural annotations and the complete interaction annotations with its silencing(s

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Albitar, Maher, Hong Zhang, Sally Agersborg, et al. "Establishing a Distinct Cytokine Signature for Multiple Myeloma Using Bone Marrow RNA and Peripheral Blood Cell-Free RNA (cfRNA)." Blood 144, Supplement 1 (2024): 3316. https://doi.org/10.1182/blood-2024-203774.

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Introduction: The combined effects of cytokines/chemokines and their receptors are believed to play a major role in determining the overall environment for plasma cell growth and the clinical course of multiple myeloma (MM). Cytokines also play a significant role in the immune response to the neoplastic plasma cells and are relevant to various therapeutic approaches. Numerous studies have evaluated various cytokines individually and correlated with clinical behavior. We used next generation sequencing (NGS) and RNA quantification along with machine learning algorithms to establish signatures b

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Luo, Yong, Xiaopeng Liu, Jingbo Lin, Weide Zhong, and Qingbiao Chen. "Development and validation of novel inflammatory response-related gene signature to predict prostate cancer recurrence and response to immune checkpoint therapy." Mathematical Biosciences and Engineering 19, no. 11 (2022): 11345–66. http://dx.doi.org/10.3934/mbe.2022528.

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<abstract> <p>The aim of this study is to construct an inflammatory response-related genes (IRRGs) signature to monitor biochemical recurrence (BCR) and treatment effects in prostate cancer patients (PCa). A gene signature for inflammatory responses was constructed on the basis of the data from the Cancer Genome Atlas (TCGA) database, and validated in external datasets. It was analyzed using receiver operating characteristic curve, BCR-free survival, Cox regression, and nomogram. Distribution analysis and external model comparison were utilized. Then, enrichment analysis, tumor mut

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Farias, Epitácio, Patrick Terrematte, and Beatriz Stransky. "Machine Learning Gene Signature to Metastatic ccRCC Based on ceRNA Network." International Journal of Molecular Sciences 25, no. 8 (2024): 4214. http://dx.doi.org/10.3390/ijms25084214.

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Clear-cell renal-cell carcinoma (ccRCC) is a silent-development pathology with a high rate of metastasis in patients. The activity of coding genes in metastatic progression is well known. New studies evaluate the association with non-coding genes, such as competitive endogenous RNA (ceRNA). This study aims to build a ceRNA network and a gene signature for ccRCC associated with metastatic development and analyze their biological functions. Using data from The Cancer Genome Atlas (TCGA), we constructed the ceRNA network with differentially expressed genes, assembled nine preliminary gene signatu

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Ahmed, Yaman B., Obada E. Ababneh, Anas A. Al-Khalili, et al. "Identification of Hypoxia Prognostic Signature in Glioblastoma Multiforme Based on Bulk and Single-Cell RNA-Seq." Cancers 16, no. 3 (2024): 633. http://dx.doi.org/10.3390/cancers16030633.

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Glioblastoma (GBM) represents a profoundly aggressive and heterogeneous brain neoplasm linked to a bleak prognosis. Hypoxia, a common feature in GBM, has been linked to tumor progression and therapy resistance. In this study, we aimed to identify hypoxia-related differentially expressed genes (DEGs) and construct a prognostic signature for GBM patients using multi-omics analysis. Patient cohorts were collected from publicly available databases, including the Gene Expression Omnibus (GEO), the Chinese Glioma Genome Atlas (CGGA), and The Cancer Genome Atlas—Glioblastoma Multiforme (TCGA-GBM), to

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Werner, Stephan, Lukas Schmidt, Virginie Marchand, et al. "Machine learning of reverse transcription signatures of variegated polymerases allows mapping and discrimination of methylated purines in limited transcriptomes." Nucleic Acids Research 48, no. 7 (2020): 3734–46. http://dx.doi.org/10.1093/nar/gkaa113.

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Abstract Reverse transcription (RT) of RNA templates containing RNA modifications leads to synthesis of cDNA containing information on the modification in the form of misincorporation, arrest, or nucleotide skipping events. A compilation of such events from multiple cDNAs represents an RT-signature that is typical for a given modification, but, as we show here, depends also on the reverse transcriptase enzyme. A comparison of 13 different enzymes revealed a range of RT-signatures, with individual enzymes exhibiting average arrest rates between 20 and 75%, as well as average misincorporation ra

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Fahey, Catherine, Anupama Reddy, Kristin Kathleen Ancell, Kerry Roe Schaffer, Brian I. Rini, and Katy Beckermann. "Examination of irAE and treatment discontinuation irAE in patients with RCC with T effector phenotype." Journal of Clinical Oncology 42, no. 16_suppl (2024): 4549. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.4549.

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4549 Background: The standard of care for renal cell carcinoma (RCC) is physician-choice of dual immunotherapy with ipilimumab/nivolumab (IO/IO) or a combination a VEGF inhibitor with immunotherapy (VEGF/IO). The IMmotion 151 trial identified gene expression signatures that differentiate likelihood of response to IO/IO (cluster 4 and 5 – T effector) versus VEGF/IO (cluster 1 and 2 - Angiogenic). Given that the T effector RNA-seq signature consists of higher expression of genes associated with inflammation, we hypothesized that patients with the T effector phenotype would have higher rates of i

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Wang, Kai, Kai Song, Zhigang Ma, et al. "Identification of EMT-related high-risk stage II colorectal cancer and characterisation of metastasis-related genes." British Journal of Cancer 123, no. 3 (2020): 410–17. http://dx.doi.org/10.1038/s41416-020-0902-y.

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Abstract Background Our laboratory previously reported an individual-level prognostic signature for patients with stage II colorectal cancer (CRC). However, this signature was not applicable for RNA-sequencing datasets. In this study, we constructed a robust epithelial-to-mesenchymal transition (EMT)- related gene pair prognostic signature. Methods Based on EMT-related genes, metastasis-associated gene pairs were identified between metastatic and non-metastatic samples. Then, we selected prognosis-associated gene pairs, which were significantly correlated with disease-free survival of stage II

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Thiede, Stephanie, Matthew Berginski, Akash Mitra, et al. "Homologous recombination deficiency (HRD) in non-small cell lung cancer: Genomic analysis using an RNA-based HRD algorithm." Journal of Clinical Oncology 41, no. 16_suppl (2023): 3123. http://dx.doi.org/10.1200/jco.2023.41.16_suppl.3123.

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3123 Background: Recent evidence has suggested that some patients with non-small cell lung cancer (NSCLC) harbor a HRD signature that represents a distinct genomic subtype that could be targeted by PARP inhibitors (PARPi). However, there is little data on HRD prevalence in NSCLC or its genomic associations. Here, we evaluated the co-occurrence of driver mutations and established immune biomarkers with an RNA-based HRD signature in a large, real-world NSCLC cohort. Methods: We analyzed data from 5119 NSCLC patients that underwent sequencing via the Tempus xT test (DNA-seq of 648 genes; RNA-seq

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Reimann, Maja, Korkut Avsar, Andrew DiNardo, et al. "The TB27 Transcriptomic Model for Predicting Mycobacterium tuberculosis Culture Conversion." Pathogens and Immunity 10, no. 1 (2025): 120–39. https://doi.org/10.20411/pai.v10i1.770.

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Rationale: Treatment monitoring of tuberculosis patients is complicated by a slow growth rate of Mycobacterium tuberculosis. Recently, host RNA signatures have been used to monitor the response to tuberculosis treatment. Objective: Identifying and validating a whole blood-based RNA signature model to predict microbiological treatment responses in patients on tuberculosis therapy. Methods: Using a multi-step machine learning algorithm to identify an RNA-based algorithm to predict the remaining time to culture conversion at flexible time points during anti-tuberculosis therapy. Results: The iden

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Motzer, Robert J., Camillo Porta, Masatoshi Eto, et al. "Biomarker analyses in patients with advanced renal cell carcinoma (aRCC) from the phase 3 CLEAR trial." Journal of Clinical Oncology 42, no. 16_suppl (2024): 4504. http://dx.doi.org/10.1200/jco.2024.42.16_suppl.4504.

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4504 Background: In the primary analysis of CLEAR, lenvatinib + pembrolizumab (L+P) significantly improved efficacy vs sunitinib (S) in treatment-naïve patients with aRCC (Motzer 2021). Results were confirmed at the final prespecified OS analysis (Motzer 2024). We report biomarker analyses from CLEAR. Methods: PD-L1 IHC 22C3 pharmDx and NGS assays (ImmunoID NeXT platform: WES and RNA-Seq) were performed on archival tumor specimens. To identify somatic alterations including mutations and copy-number variations, paired PBMC samples were used as reference. For RNA-Seq/IHC-derived analyses, a cont

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Lan, Yunyun, Juan Su, Yaxin Xue, Lulu Zeng, Xun Cheng, and Liyi Zeng. "Analysing a Novel RNA-Binding-Protein-Related Prognostic Signature Highly Expressed in Breast Cancer." Journal of Healthcare Engineering 2021 (October 18, 2021): 1–15. http://dx.doi.org/10.1155/2021/9174055.

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Background. Breast cancer (BRCA) is one of the most common cancers and the leading cause of cancer-related death in women. RNA-binding proteins (RBPs) play an important role in the emergence and pathogenesis of tumors. The target RNAs of RBPs are very diverse; in addition to binding to mRNA, RBPs also bind to noncoding RNA. Noncoding RNA can cause secondary structures that can bind to RBPs and regulate multiple processes such as splicing, RNA modification, protein localization, and chromosomes remodeling, which can lead to tumor initiation, progression, and invasion. Methods. (1) BRCA data wer

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Zhong, Shanliang, Zhenzhong Lin, Huanwen Chen, Ling Mao, Jifeng Feng, and Siying Zhou. "The m6A-related gene signature for predicting the prognosis of breast cancer." PeerJ 9 (June 4, 2021): e11561. http://dx.doi.org/10.7717/peerj.11561.

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N6-methyladenosine (m6A) modification has been shown to participate in tumorigenesis and metastasis of human cancers. The present study aimed to investigate the roles of m6A RNA methylation regulators in breast cancer. We used LASSO regression to identify m6A-related gene signature predicting breast cancer survival with the datasets downloaded from Gene Expression Omnibus and The Cancer Genome Atlas (TCGA). RNA-Seq data of 3409 breast cancer patients from GSE96058 and 1097 from TCGA were used in present study. A 10 m6A-related gene signature associated with prognosis was identified from 22 m6A

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Tian, Ye, Jing Dong, and Lin Li. "Bridging Pyroptosis and Immunity: A Comprehensive Study of the Pyroptosis-Related Long Non-Coding RNA Signature in Breast Cancer." Life 13, no. 7 (2023): 1599. http://dx.doi.org/10.3390/life13071599.

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Breast cancer continuously poses serious clinical challenges to human health due to its intrinsic heterogenicity and evolving drug resistance. Recently, increasing evidence has shown that pyroptosis, known as a programmed and inflammatory form of cell death, participates in tumorigenesis, progression, and remodeling of the tumor immune microenvironment (TIME). However, a comprehensive insight into pyroptosis-related signatures for breast cancer remains elusive. The current study established a pyroptosis-related lncRNA signature using transcriptome data and corresponding clinical information fr

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Zhou, J., and H. Ma. "OS1.2 Development and Validation of a RNA-Seq Based Prognostic Signature in Neuroblastoma." Neuro-Oncology 21, Supplement_3 (2019): iii5. http://dx.doi.org/10.1093/neuonc/noz126.015.

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Abstract BACKGROUND Credible prognostic stratification remains a challenge for neuroblastoma (NBL) with variable clinical manifestations. RNA expression signatures might predict the outcomes; notwithstanding, independent cross-platform validation is still rare. MATERIAL AND METHODS expression data were obtained from NBL patients and then analyzed. In TARGET-NBL data, an RNA-based prognostic signature was developed and validated. Survival prediction was assessed using a time-dependent receiver operating characteristic (ROC) curve. Functional enrichment analysis of the RNAs was conducted using b

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Zhong, Cheng, Dongliang Yang, Liping Zhong, et al. "Single-cell and bulk RNA sequencing reveals Anoikis related genes to guide prognosis and immunotherapy in osteosarcoma." Scientific Reports 13, no. 1 (2023). http://dx.doi.org/10.1038/s41598-023-47367-3.

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AbstractAnoikis resistance, a notable factor in osteosarcoma, plays a significant role in tumor invasion and metastasis. This study seeks to identify a distinct gene signature that is specifically associated with the anoikis subcluster in osteosarcoma. Clinical, single-cell, and transcriptional data from TARGET and GEO datasets were used to develop a gene signature for osteosarcoma based on the anoikis subcluster. Univariate Cox and LASSO regression analyses were employed. The signature's predictive value was evaluated using time-dependent ROC and Kaplan–Meier analyses. Functional enrichment a

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Zhao, Xudong, Tong Liu, and Guohua Wang. "Ensemble classification based signature discovery for cancer diagnosis in RNA expression profiles across different platforms." Briefings in Bioinformatics, May 24, 2022. http://dx.doi.org/10.1093/bib/bbac185.

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Abstract Molecular signatures have been excessively reported for diagnosis of many cancers during the last 20 years. However, false-positive signatures are always found using statistical methods or machine learning approaches, and that makes subsequent biological experiments fail. Therefore, signature discovery has gradually become a non-mainstream work in bioinformatics. Actually, there are three critical weaknesses that make the identified signature unreliable. First of all, a signature is wrongly thought to be a gene set, each component of which keeps differential expressions between or amo

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Sahu, Divya, Shinn-Ying Ho, Hsueh-Fen Juan, and Hsuan-Cheng Huang. "High-risk, Expression-Based Prognostic Long Noncoding RNA Signature in Neuroblastoma." JNCI Cancer Spectrum 2, no. 2 (2018). http://dx.doi.org/10.1093/jncics/pky015.

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Abstract Background Current clinical risk factors stratify patients with neuroblastoma (NB) for appropriate treatments, yet patients with similar clinical behaviors evoke variable responses. MYCN amplification is one of the established drivers of NB and, when combined with high-risk displays, worsens outcomes. Growing high-throughput transcriptomics studies suggest long noncoding RNA (lncRNA) dysregulation in cancers, including NB. However, expression-based lncRNA signatures are altered by MYCN amplification, which is associated with high-risk, and patient prognosis remains limited. Methods We

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Ren, Xin, Zhuxiao Feng, Xiaodong Ma, et al. "m6A/m1A/m5C-Associated Methylation Alterations and Immune Profile in MDD." Molecular Neurobiology, March 8, 2024. http://dx.doi.org/10.1007/s12035-024-04042-6.

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AbstractMajor depressive disorder (MDD) is a prevalent psychiatric condition often accompanied by severe impairments in cognitive and functional capacities. This research was conducted to identify RNA modification-related gene signatures and associated functional pathways in MDD. Differentially expressed RNA modification-related genes in MDD were first identified. And a random forest model was developed and distinct RNA modification patterns were discerned based on signature genes. Then, comprehensive analyses of RNA modification-associated genes in MDD were performed, including functional ana

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Deng, Zhili, Fangfen Liu, Mengting Chen, et al. "Keratinocyte-Immune Cell Crosstalk in a STAT1-Mediated Pathway: Novel Insights Into Rosacea Pathogenesis." Frontiers in Immunology 12 (July 5, 2021). http://dx.doi.org/10.3389/fimmu.2021.674871.

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Rosacea is a common chronic inflammatory condition that mainly affects the central face. However, the molecular background of the normal central face and the transcriptional profiling and immune cell composition of rosacea lesions remain largely unknown. Here, we performed whole-skin and epidermal RNA-seq of central facial skin from healthy individuals, lesions and matched normal skin from rosacea patients. From whole-skin RNA-seq, the site-specific gene signatures for central facial skin were mainly enriched in epithelial cell differentiation, with upregulation of the activator protein-1 (AP1

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El-Sharkawy, Yasser H., Sherif Elbasuney, Sara M. Radwan, Mostafa A. Askar, Samar H. Rizk, and Gharieb S. El-Sayyad. "The potentials of nonlinear polarization with hyperspectral imaging of RNA for hepatocellular carcinoma early diagnosis." Egyptian Journal of Medical Human Genetics 25, no. 1 (2024). http://dx.doi.org/10.1186/s43042-024-00541-2.

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Abstract Background Most cancers acquire numerous genetic changes in proto-oncogenes as well as tumor-suppressor genes. Cancer's early diagnosis remains a challenge. Recently, nonlinear polarization has revealed the potential as a promising tool for early cancer diagnosis. Laser-induced nonlinear polarization can offer a novel fingerprint signature. Methods In this study, nonlinear polarization was adopted for the characterization of both DNA and RNA samples from healthy volunteers. Total DNA and RNA were illuminated with a 656-nm LED source, and the resonance frequencies (scattered and re-emi

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Zhao, Chunxia, Yulu Wang, Famei Tu, et al. "A Prognostic Autophagy-Related Long Non-coding RNA (ARlncRNA) Signature in Acute Myeloid Leukemia (AML)." Frontiers in Genetics 12 (June 30, 2021). http://dx.doi.org/10.3389/fgene.2021.681867.

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BackgroundSome studies have proven that autophagy and lncRNA play important roles in AML. Several autophagy related lncRNA signatures have been shown to affect the survival of patients in some other cancers. However, the role of autophagy related lncRNA in AML has not been explored yet. Hence, this study aims to find an autophagy related lncRNA signature that can affect survival for AML patients.MethodA Pearson correlation analysis, a Kaplan–Meier survival curve, a univariate cox regression, and a multivariate cox regression were performed to establish an autophagy related lncRNA signature. A

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